Markers + reference

Sinocrassula

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 606 0.0083 0.99 56.4 yes View details
rpoB-trnC-GCA LSC 1110 0.0040 0.90 58.6 yes View details
psbM-trnD-GUC LSC 1044 0.0048 0.99 62.5 yes View details
psbZ-trnG-UCC LSC 627 0.0901 0.92 80.6 yes View details
psaA-ycf3 LSC 593 0.0068 0.99 63.7 yes View details
trnT-UGU-trnL-UAA LSC 410 0.0098 1.00 60.4 yes View details
rbcL LSC 1428 0.0000 1.00 32.7 yes View details
rbcL-accD LSC 675 0.0062 0.96 62.0 yes View details
ycf1 IRb 1143 0.0009 1.00 59.3 no View details
ycf1 SSC 5136 0.0029 1.00 50.5 yes View details
trnG-UCC LSC 71 0.1408 1.00 72.5 yes View details
psaJ-rpl33 LSC 456 0.0070 0.95 64.4 yes View details
ndhF-rpl32 SSC 610 0.0017 0.94 64.4 yes View details
ycf4-cemA LSC 650 0.0016 0.94 64.3 yes View details
rps19-rpl2 IRb 54 0.0185 1.00 63.1 yes View details
rpl2-rps19 IRa 54 0.0185 1.00 61.9 yes View details
ndhK LSC 768 0.0000 0.97 61.4 yes View details
psbH-petB LSC 715 0.0042 1.00 61.2 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AGATCGATGAGCATTTTTGATCA AGACTTTCCTTCCTTTTTGGCT 2623 1.000 40.3
trnK-UUU_p2 trnK-UUU AGATCGATGAGCATTTTTGATCA AGACTTTCCTTCCTTTTTGGC 2623 1.000 40.3
trnK-UUU_p3 trnK-UUU AGATCGATGAGCATTTTTGATCA GACTTTCCTTCCTTTTTGGCT 2622 1.000 40.3
trnK-UUU_p4 trnK-UUU AGATCGATGAGCATTTTTGATCA ACTTTCCTTCCTTTTTGGCTTG 2621 1.000 40.3
trnK-UUU_p5 trnK-UUU AGATCGATGAGCATTTTTGATCAA AGACTTTCCTTCCTTTTTGGCT 2623 1.000 40.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGTTCGGAATACAAAGAAAACCG 729–731 1.000 56.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGTTCGGAATACAAAGAAAACCG 728–730 1.000 56.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGTTCGGAATACAAAGAAAACCG 747–749 1.000 55.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TGTTCGGAATACAAAGAAAACCG 783–785 1.000 54.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GAATCGCTCGTACAACGGAT TGTTCGGAATACAAAGAAAACCG 752–754 1.000 54.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG CCGGATTTGAACTGGGGAAA 1167–1276 1.000 82.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCGTCAAGCCATGA CCGGATTTGAACTGGGGAAA 1166–1275 1.000 82.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG AGTCTTGTGTTGATCAGGCG 1191–1300 1.000 81.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG GTCTTGTGTTGATCAGGCGA 1190–1299 1.000 81.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCCGTCAAGCCATG TCTTGTGTTGATCAGGCGAC 1189–1298 1.000 81.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCAGTAGGAACTAGAATGA TCAATTGGTAAGAGCACCGC 1158–1168 1.000 48.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AAGGCAGTAGGAACTAGAATGA TCAATTGGTAAGAGCACCGC 1159–1169 1.000 46.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGCAGTAGGAACTAGAATGAA TCAATTGGTAAGAGCACCGC 1158–1168 1.000 46.8
psbM-trnD-GUC_p4 psbM-trnD-GUC AAAGGCAGTAGGAACTAGAATGA TCAATTGGTAAGAGCACCGC 1160–1170 1.000 44.5
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGGCAGTAGGAACTAGAATGAA TCAATTGGTAAGAGCACCGC 1159–1169 1.000 44.5
psbZ-trnG-UCC_p1 psbZ-trnG-UCC GTTTCCGTTTTTCTGGCTCG CTTGAGGTCACGGGTTCAAA 1560–1801 1.000 84.8
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTTTCTGGCTCGGCTATTCC CTTGAGGTCACGGGTTCAAA 1552–1793 1.000 84.7
psbZ-trnG-UCC_p3 psbZ-trnG-UCC CAGCCATCTCTCCGAAAGAC CGTTGTTTTTCGACCGGAAG 1715–1956 1.000 84.2
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GTTTCCGTTTTTCTGGCTCG CGTTGTTTTTCGACCGGAAG 1896–2137 1.000 84.1
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TTTTCTGGCTCGGCTATTCC CGTTGTTTTTCGACCGGAAG 1888–2129 1.000 84.0
trnG-UCC_p1 trnG-UCC TTTGCTTCTCCTGACGGTTG CTTGAGGTCACGGGTTCAAA 985–1226 1.000 84.5
trnG-UCC_p2 trnG-UCC TTTGCTTCTCCTGACGGTTG CGTTGTTTTTCGACCGGAAG 1321–1562 1.000 82.9
trnG-UCC_p3 trnG-UCC TTTGCTTCTCCTGACGGTTG CAGGGGCAACAAGATCAAGT 1227–1468 1.000 82.7
trnG-UCC_p4 trnG-UCC TGGGCGTATCAAGAACGAAA CGTTGTTTTTCGACCGGAAG 612 0.500 56.2
trnG-UCC_p5 trnG-UCC TGGGCGTATCAAGAACGAAA CTTGAGGTCACGGGTTCAAA 276 0.500 56.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Sinocrassula densirosulata NC_053955.1 151773 View on NCBI ↗
Sinocrassula indica MN794334.1 151755 View on NCBI ↗